8EFK | pdb_00008efk

Structure of Lates calcarifer DNA polymerase theta polymerase domain with hairpin DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structural basis of DNA polymerase theta mediated DNA end joining.

Li, C.Zhu, H.Jin, S.Maksoud, L.M.Jain, N.Sun, J.Gao, Y.

(2023) Nucleic Acids Res 51: 463-474

  • DOI: https://doi.org/10.1093/nar/gkac1201
  • Primary Citation Related Structures: 
    8EF9, 8EFC, 8EFK

  • PubMed Abstract: 

    DNA polymerase θ (Pol θ) plays an essential role in the microhomology-mediated end joining (MMEJ) pathway for repairing DNA double-strand breaks. However, the mechanisms by which Pol θ recognizes microhomologous DNA ends and performs low-fidelity DNA synthesis remain unclear. Here, we present cryo-electron microscope structures of the polymerase domain of Lates calcarifer Pol θ with long and short duplex DNA at up to 2.4 Å resolution. Interestingly, Pol θ binds to long and short DNA substrates similarly, with extensive interactions around the active site. Moreover, Pol θ shares a similar active site as high-fidelity A-family polymerases with its finger domain well-closed but differs in having hydrophilic residues surrounding the nascent base pair. Computational simulations and mutagenesis studies suggest that the unique insertion loops of Pol θ help to stabilize short DNA binding and assemble the active site for MMEJ repair. Taken together, our results illustrate the structural basis of Pol θ-mediated MMEJ.


  • Organizational Affiliation
    • Department of Biosciences, Rice University, Houston, TX 77005, USA.

Macromolecule Content 

  • Total Structure Weight: 103.45 kDa 
  • Atom Count: 5,020 
  • Modeled Residue Count: 613 
  • Deposited Residue Count: 888 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lates calcarifer DNA polymerase theta864Lates calcariferMutation(s): 0 
EC: 2.7.7.7
UniProt
Find proteins for A0A4W6BKE5 (Lates calcarifer)
Explore A0A4W6BKE5 
Go to UniProtKB:  A0A4W6BKE5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4W6BKE5
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*TP*GP*GP*CP*TP*TP*TP*TP*GP*CP*CP*(2DA))-3')B [auth E]24Lates calcarifer
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Cancer SocietyUnited StatesRSG-22-082-01-DMC
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRR170062

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Database references
  • Version 1.2: 2023-02-01
    Changes: Database references
  • Version 1.3: 2024-06-19
    Changes: Data collection
  • Version 1.4: 2025-06-04
    Changes: Data collection, Structure summary